The long range goal of these studies is to delineate viral determinants of lentivirus disease and persistence. Genetic diversity is a hallmark of lentivirus infections. In vivo populations of virus are comprised of a heterogeneous mix of related genotypic and phenotypic variants, each with the potential to become dominant in the face of environmental change. The goal of this study is to determine if virus variants with altered replication fitness are preferentially selected during periods of immune maturation and clinical latency. As lentiviruses are already known to vary in env with disease progression, this study may provide the first definitive evidence that other genes are selected in association with changes in the host immune environment. This pilot study will utilize the well-characterized equine infectious anemia virus (EIAV) model to test the hypothesis that immune maturation and the onset of clinical quiescence are associated with selection of viral variants with decreased Rev activity. In the first specific aim, retrospective samples from EIAV-infected horses will be used in longitudinal and cross-sectional analyses of Rev quasispecies during clinical disease. Genetic and computational tools will establish the general patterns of quasispecies evolution at different stages of clinical disease and immune maturation. In the second specific aim, Rev genotypes identified in Specific Aim 1 will be functionally characterized in transient expression assays. The quasispecies Rev phenotype will be determined using a weighted average of the activity of individual variants, and statistical analyses will determine if changes in quasispecies Rev phenotype correlate with specific stages of clinical disease. Rev chimeric proviruses will be constructed to determine the effect of Rev variation on virus replication. The third specific aim will develop a mathematical model of phenotype variation and immune maturation to explore in silico the hypothesis that less fit variants may be selected in a host with a mature immune response. Completion of these studies will demonstrate the importance of secondary loci in disease progression, reveal the biological relevance and utility of multi-locus modets, and form a basis for more realistic and complex models that include additional virus and host parameters of disease progression.